Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor

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1. Version published to 10.1038/s41588-020-00731-9

   Oct 19, 2020
2. 

   ScreenIT

   Jul 21, 2020

   SciScore for 10.1101/2020.07.19.210955: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Fixed cells were incubated with rabbit anti-FLAG antibody (1:250 dilution, Thermo Fisher) overnight, washed and then stained with anti-rabbit Alexa Fluor 680 (1:500 dilution, Thermo Fisher).	anti-FLAG suggested: None anti-rabbit suggested: None
   Cell lysates were analyzed by Western blots with C-terminal anti-ACE2 antibody (Abcam), and the amounts of recombinant ACE2-GFP and dACE2-GFP proteins in lysates were quantified by densitometry analysis (Imagelab, BD Biosciences) of Western blots.	anti-ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells listed in Table S3 were infected in …

   SciScore for 10.1101/2020.07.19.210955: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Fixed cells were incubated with rabbit anti-FLAG antibody (1:250 dilution, Thermo Fisher) overnight, washed and then stained with anti-rabbit Alexa Fluor 680 (1:500 dilution, Thermo Fisher).	anti-FLAG suggested: None anti-rabbit suggested: None
   Cell lysates were analyzed by Western blots with C-terminal anti-ACE2 antibody (Abcam), and the amounts of recombinant ACE2-GFP and dACE2-GFP proteins in lysates were quantified by densitometry analysis (Imagelab, BD Biosciences) of Western blots.	anti-ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells listed in Table S3 were infected in duplicates or triplicates with SeV (7.5×105 CEID50/ml) for 12 or 24 hrs as previously described19–21. Infections with SARS-CoV-2 in colon cancer cell lines (Caco2 and T84) and lung cancer cell line (Calu3) and colon and ileum organoid cultures were previously described23.	Caco2 suggested: None
   Organoids were infected with 3×105 FFU of the virus, based on titers in Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   T84 and Caco-2 cells were treated with IFN-γ (2 ng/ml) for 48 hrs, followed by cell harvesting, RNA extraction and expression analysis.	Caco-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Cell lines were either used within 6 months after purchase or were periodically authenticated by microsatellite fingerprinting (AmpFLSTR Identifiler, Thermo Fisher) by the Cancer Genomics Research Laboratory/NCI).	Cancer Genomics Research Laboratory/NCI suggested: None
   RNA-seq analysis of data from NCBI Sequence Read Archive (SRA) and TCGA: RNA-seq datasets (Table S6) were downloaded from NCBI SRA using SRA tools.	NCBI Sequence Read Archive suggested: (NCBI Sequence Read Archive (SRA, RRID:SCR_004891)
   The FASTQ files were compressed using GZIP and aligned with STAR version 7.1.3a to the GRChg38/hg38 genome assembly.	GZIP suggested: (Gzip, RRID:SCR_009291) STAR suggested: (STAR, RRID:SCR_015899)
   BAM files were indexed and sliced using SAM tools to include 51.6 Kb of the ACE2 genomic region (chrX:15,556,393-15,608,016, hg38).	SAM suggested: (SAM, RRID:SCR_010951)
   https://www.cbioportal.org/).	https://www.cbioportal.org/ suggested: (cBioPortal, RRID:SCR_014555)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.07.19.210955 on bioRxiv

   Jul 20, 2020